Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) Collection 6 cloud observations (MYD06) at 1 km are collocated with daytime CloudSat‐Cloud‐Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) (C‐C) cloud vertical structures (2B‐CLDCLASS‐LIDAR). For 2007–2010, over 267 million C‐C cloud profiles are used to (1) validate MODIS cloud mask and cloud multilayer flag and (2) cross‐reference between C‐C cloud types and MODIS cloud regimes defined by joint histograms of cloud top pressure (CTP) and cloud optical depth (τ). Globally, of total observations, C‐C reports 27.1% clear and 72.9% cloudy, whereas MODIS reports 30.0% confidently clear and 58.7% confidently cloudy, with the rest 7.1% as probably clear and 4.2% as probably cloudy. Agreement between MODIS and C‐C is 77.8%, with 20.9% showing both clear and 56.9% showing both cloudy. The 9.1% of observations are clear in MODIS but cloudy in C‐C, indicating clouds missed by MODIS; 1.8% of observations are cloudy in MODIS but clear in C‐C, likely due to aerosol/dust or surface snow layers misidentified by MODIS. C‐C reports 47.4/25.5% single‐layer/multilayer clouds, while MODIS reports 26.7/14.0%. For C‐C single‐layer clouds, ~90% of tropical MODIS high (CTP < 440 hPa) and optically thin (τ < 3.6) clouds are identified as cirrus and ~60% of high and optically thick (τ > 23) clouds are recognized as deep convective in C‐C. Approximately 70% of MODIS low‐level (CTP > 680 hPa) clouds are classified as stratocumulus in C‐C regardless of region and optical thickness. No systematic relationship exists between MODIS middle‐level (680 < CTP < 440 hPa) clouds and C‐C cloud types, largely due to different definitions adopted. Key Points The 20.9/56.9% of collocated MODIS and C‐C are identified as clear/cloudy; 9.1/1.8% are clear/cloudy in MODIS but cloudy/clear in C‐C The 17.7/7.7% of MODIS/C‐C observation are both single layer/multilayer; 8.7/6.3% are single layer/multilayer in MODIS but multilayer/single layer in C‐C For single‐layer cases, ~70% of MODIS low‐level clouds are classified as Sc in C‐C regardless of optical thickness